IlvD - Revision history

Jstuelk: /* Database entries */

2015-07-30T13:10:48Z

‎Database entries

Jstuelk at 13:10, 30 July 2015

2015-07-30T13:10:33Z

Jstuelk: /* References */

2015-07-30T13:01:28Z

‎References

134.76.70.252 at 14:09, 17 April 2014

2014-04-17T14:09:10Z

134.76.70.252 at 09:25, 17 April 2014

2014-04-17T09:25:10Z

134.76.38.147 at 14:00, 2 April 2014

2014-04-02T14:00:38Z

Jstuelk at 16:52, 5 March 2014

2014-03-05T16:52:43Z

134.76.70.252 at 11:02, 7 January 2014

2014-01-07T11:02:36Z

Jstuelk at 12:22, 22 December 2013

2013-12-22T12:22:13Z

Jstuelk at 18:42, 13 December 2013

2013-12-13T18:42:04Z

← Older revision		Revision as of 13:10, 30 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate, 2,3-dihydroxy-3-methylpentanoate) <br/><br/>~~	+	{{#bank: IlvD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ilvD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| dihydroxy-acid dehydratase <br/>(2,3-dihydroxy-3-methylbutanoate,<br/> 2,3-dihydroxy-3-methylpentanoate)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| biosynthesis of branched-chain amino acids~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU21870 ilvD]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ilvD ilvD]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 59 kDa, 5.315~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1674 bp, 558 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[brxA]]'', ''[[ypgR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU21870 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU21870 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU21870 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ilvD_context.gif]]~~
−	~~<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>~~
−	\|-
−	\|colspan="2" \|'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ilvD_2300762_2302438_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ilvD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU21870]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biosynthesis/ acquisition of amino acids]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU21870
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU21870&redirect=T BSU21870]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ilvD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11532]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' 2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H<sub>2</sub>O (according to Swiss-Prot)
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU21870&redirect=T BSU21870]
−
−	* '''Structure:''' http://www.rcsb.org/pdb/explore/explore.do?structureId=2GP4 2GP4 (apo form of 6-phosphogluconate dehydratase from ''Shewanella oneidensis'', 33% identity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P51785 P51785]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU21870]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.9 4.2.1.9]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[ilvD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/15060025 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ilvD_2300762_2302438_-1 ilvD] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−	** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/18083814 PubMed2]
−
−	* '''Additional information:'''
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 3104 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 1545 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 4271 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 1398 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 2083 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:''' pGP522 (in [[pAC5]]), pGP235 (in [[pAC5]]), both available in [[Jörg Stülke]]'s lab; a series of promoter deletions in [[pAC6]] is available in [[Jörg Stülke]]'s lab
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>18083814,12618455,15060025,12107147, 24163341 15378759 26220295</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 94: / Line 94: @@
 * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU21870&redirect=T BSU21870]
-* '''Structure:'''
+* '''Structure:''' http://www.rcsb.org/pdb/explore/explore.do?structureId=2GP4 2GP4 (apo form of 6-phosphogluconate dehydratase from ''Shewanella oneidensis'', 33% identity)
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P51785 P51785]

@@ Line 146: / Line 146: @@
 =References=
-<pubmed>18083814,12618455,15060025,12107147, 24163341 15378759</pubmed>
+<pubmed>18083814,12618455,15060025,12107147, 24163341 15378759 26220295</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 123: / Line 123: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 3104 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 1545 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

@@ Line 121: / Line 121: @@
 * '''Additional information:'''
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ilvD.html]
@@ Line 91: / Line 92: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 42: / Line 42: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}}
+{{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 117: / Line 118: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 138: / Line 140: @@
 =References=
-<pubmed>18083814,12618455,15060025,12107147, 24163341</pubmed>
+<pubmed>18083814,12618455,15060025,12107147, 24163341 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 16: / Line 16: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU21870 ilvD]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Ile, Leu, Val], [http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html Coenzyme A]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ilvD ilvD]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 59 kDa, 5.315

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 66: / Line 62: @@
 === Additional information===
 =The protein=
@@ Line 84: / Line 77: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 114: / Line 107: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ilvD_2300762_2302438_-1 ilvD] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 131: / Line 124: @@
 * '''Expression vector:'''
-* '''lacZ fusion:''' pGP522 (in [[pAC5]]), pGP235 (in [[pAC5]]), both available in [[Stülke]] lab; a series of promoter deletions in [[pAC6]] is available in [[Stülke]] lab
+* '''lacZ fusion:''' pGP522 (in [[pAC5]]), pGP235 (in [[pAC5]]), both available in [[Jörg Stülke]]'s lab; a series of promoter deletions in [[pAC6]] is available in [[Jörg Stülke]]'s lab
 * '''GFP fusion:'''
@@ Line 145: / Line 138: @@
 =References=
-<pubmed>18083814,12618455,15060025,12107147, </pubmed>
+<pubmed>18083814,12618455,15060025,12107147, 24163341</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1674 bp, 558 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yphP]]'', ''[[ypgR]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[brxA]]'', ''[[ypgR]]''
 |-
 |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU21870 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU21870 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU21870 DNA_with_flanks]